Setting permissions once, as @DMA57361 explains, is no real solution, as ACL problems may still occur later and suddenly there is a subtree of the folder structure that is inaccessible e.g. to your backup routine. When unnoticed, this may cause a loss of data and when noticed it may at least cause a huge annoyance.

Think e.g. about a 100.000 files personal drive of which backups where made using robocopy or rsync and hard-link copies of the folder structure for preserving older versions without wasting storage space. If some ACL conflict occurs, recovering the permissions in windows requires iterating over all those maybe millions of file system nodes, which takes... forever.

So for a data-only drive on a single-user system like a notebook fully disabling any form of permissions would sometimes be preferable.

Currently I am trying to use UDF as my backup file system. For all I know it doesn't have journalling but compared to FAT32 it doesn't have problems with files beyond 4 GB.

Windows can format drives in UDF using in the command line e.g.

format E: /FS:UDF

As of today, Windows 7 uses by default UDF 2.01, but the /R flag allows selecting a specific version up to 2.50.

Sadly though I found barely any information on experiences with UDF on hard drives other than people using it as a cross-platform file system as a more modern alternative to FAT32.